An arginyl residue in rice UDP-arabinopyranose mutase is required for catalytic activity and autoglycosylation

Structures of the NDP-pyranose mutase belonging to glycosyltransferase family 75 reveal residues important for Mn2+ coordination and substrate binding

Members of glycosyltransferase family 75 (GT75) not only reversibly catalyze the autoglycosylation of a conserved arginine residue with specific NDP-sugars but also exhibit NDP-pyranose mutase activity that reversibly converts specific NDP-pyranose to NDP-furanose. The latter activity provides valuable NDP-furanosyl donors for glycosyltransferases and requires a divalent cation as a cofactor instead of FAD used by UDP-D-galactopyranose mutase. However, details of the mechanism for NDP-pyranose mutase activity are not clear. Here we report the first crystal structures of GT75 family NDP-pyranose mutases. The novel structures of GT75 member MtdL in complex with Mn²⁺ and GDP, GDP-D-glucopyranose, GDP-L-fucopyranose, GDP-L-fucofuranose, respectively, combined with site-directed mutagenesis studies, reveal key residues involved in Mn²⁺ coordination, substrate binding, and catalytic reactions. We also provide a possible catalytic mechanism for this unique type of NDP-pyranose mutase. Taken together, our results highlight key elements of an enzyme family important for furanose biosynthesis.

Not Just a Simple Sugar: Arabinose Metabolism and Function in Plants

Growth, development, structure as well as dynamic adaptations and remodeling processes in plants are largely controlled by properties of their cell walls. These intricate wall structures are mostly made up of different sugars connected through specific glycosidic linkages but also contain many glycosylated proteins. A key plant sugar that is present throughout the plantae, even before the divergence of the land plant lineage, but is not found in animals, is l-arabinose (l-Ara). Here, we summarize and discuss the processes and proteins involved in l-Ara de novo synthesis, l-Ara interconversion, and the assembly and recycling of l-Ara-containing cell wall polymers and proteins. We also discuss the biological function of l-Ara in a context-focused manner, mainly addressing cell wall-related functions that are conferred by the basic physical properties of arabinose-containing polymers/compounds. In this article we explore these processes with the goal of directing future research efforts to the many exciting yet unanswered questions in this research area.

LSPR based on-chip detection of dengue NS1 antigen in whole blood

The development of a biosensor for rapid and quantitative detection of the dengue virus continues to remain a challenge. We report a lab-on-chip device that combines membrane-based blood plasma separation and a localized surface plasmon resonance (LSPR) based biosensor for on-chip detection of dengue NS1 antigen from a few drops of blood. The LSPR effect is realized by irradiating UV-NIR light having a spectral peak at 655 nm onto nanostructures fabricated via thermal annealing of a thin metal film. We study the effect of the resulting metal nanostructures on the LSPR performance in terms of sensitivity and limit of detection, by annealing silver films at temperatures ranging from 100 to 500 °C. The effect of annealing temperature on the nanostructure size and uniformity and the resulting optical characteristics are investigated. Further, the binding between non-targeted blood plasma proteins and NS1-antibody-functionalized nanostructures on the LSPR performance is studied by considering different blocking mechanisms. Using a nanostructure annealed at 200 °C and 2X-phosphate buffer saline with 0.05% Tween-20 as the blocking buffer, from 10 μL of whole blood, the device can detect NS1 antigen at a concentration as low as 0.047 μg mL-1 within 30 min. Finally, we demonstrate the detection of NS1 in the blood samples of dengue-infected patients and validate our results with those obtained from the gold-standard ELISA test.

A Novel Reversibly Glycosylated Polypeptide-2 of Bee Pollen from Rape (Brassica napus L.): Purification and Characterization

BACKGROUND

Reversibly glycosylated polypeptide (RGP), a kind of hydrosoluble and plasmodesmal-associated protein found in plants, plays a crucial role in the development of pollen.

OBJECTIVE

A novel RGP 2 was isolated and identified from rape (Brassica napus L.) bee pollen.

METHODS

RGP2 was isolated and purified by ion-exchange column and gel filtration chromatography, and characterized by MALDI-TOF-MS, LC-MS, immunological histological chemistry, and transmission electron microscope.

RESULTS

Our results indicated that the RGP2 is an acidic protein (pI=5.46) with the molecular weight 42388 Da. It contained 17 kinds of amino acids, among which aspartic acid had the highest amount (71.56 mg/g). Homologous alignment of amino acid sequence results showed that RGP2 was 80.33%, 85.02%, 86.06%, and 88.93% identical to Arabidopsis thaliana RGP2 (AtRGP2), Oryza sativa RGP (OsRGP), Triticum aestivum RGP (TaRGP), and Zea maize RGP (ZmRGP), respectively. The localization results showed that RGP2 in rape anther existed in exine and intine of anther cells of rape flower by immunological histological chemistry and the subcellular localization identified that RGP2 appeared around the Golgi apparatus in cytoplasm by transmission electron microscope.

CONCLUSION

RGP2 has a highly conserved sequence of amino acid residues and potential glycosylation sites.

Molecular characteristics of plant UDP-arabinopyranose mutases

l-arabinofuranose is a ubiquitous component of the cell wall and various natural products in plants, where it is synthesized from cytosolic UDP-arabinopyranose (UDP-Arap). The biosynthetic machinery long remained enigmatic in terms of responsible enzymes and subcellular localization. With the discovery of UDP-Arap mutase in plant cytosol, the demonstration of its role in cell-wall arabinose incorporation and the identification of UDP-arabinofuranose transporters in the Golgi membrane, it is clear that the cytosolic UDP-Arap mutases are the key enzymes converting UDP-Arap to UDP-arabinofuranose for cell wall and natural product biosynthesis. This has recently been confirmed by several genotype/phenotype studies. In contrast to the solid evidence pertaining to UDP-Arap mutase function in vivo, the molecular features, including enzymatic mechanism and oligomeric state, remain unknown. However, these enzymes belong to the small family of proteins originally identified as reversibly glycosylated polypeptides (RGPs), which has been studied for >20 years. Here, we review the UDP-Arap mutase and RGP literature together, to summarize and systemize reported molecular characteristics and relations to other proteins.

Exceptionally versatile – arginine in bacterial post-translational protein modifications

Post-translational modifications (PTM) are the evolutionary solution to challenge and extend the boundaries of genetically predetermined proteomic diversity. As PTMs are highly dynamic, they also hold an enormous regulatory potential. It is therefore not surprising that out of the 20 proteinogenic amino acids, 15 can be post-translationally modified. Even the relatively inert guanidino group of arginine is subject to a multitude of mostly enzyme mediated chemical changes. The resulting alterations can have a major influence on protein function. In this review, we will discuss how bacteria control their cellular processes and develop pathogenicity based on post-translational protein-arginine modifications.

Identification and characterization of some putative genes involved in arabinoxylan biosynthesis in Plantago ovata

Plantago ovata is an important source of Psyllium (Isabgol), which swells upon contact with water forming mucilaginous mass, largely composed of arabinoxylans. In this study, we analyzed the expression pattern of arabinoxylan biosynthetic pathway genes at different stages of seed development in P. ovata. Besides, arabinoxylans were quantified at different stages of seed development in water extractable and water unextractable fractions. The expression analysis revealed 5-8 fold increase in the levels of expression of some genes involved in arabinoxylan biosynthetic pathway such as UDP-arabinopyranose mutase, UDP-xylosyltransferase 2 and xylan glucuronosyltransferase at 15 days after pollination stage in seed. The xylose and arabinose units were analyzed at different stages of seed development and also in water-soluble (cold water and hot water), alkali and ethanolic fractions. The concentration of xylose and arabinose units increased steadily after pollination. Overall, alkali extract had high concentration of xylose (0.70 ± 0.022 mg/g) and arabinose units (0.10 ± 0.01 mg/g) at 15 days after pollination stage.

UDP-arabinopyranose mutase gene expressions are required for the biosynthesis of the arabinose side chain of both pectin and arabinoxyloglucan, and normal leaf expansion in Nicotiana tabacum

Plant cell walls are composed of polysaccharides such as cellulose, hemicelluloses, and pectins, whose location and function differ depending on plant type. Arabinose is a constituent of many different cell wall components, including pectic rhamnogalacturonan I (RG-I) and II (RG-II), glucuronoarabinoxylans (GAX), and arabinoxyloglucan (AXG). Arabinose is found predominantly in the furanose rather than in the thermodynamically more stable pyranose form. The UDP-arabinopyranose mutases (UAMs) have been demonstrated to convert UDP-arabinopyranose (UDP-Arap) to UDP-arabinofuranose (UDP-Araf) in rice (Oryza sativa L.). The UAMs have been implicated in polysaccharide biosynthesis and developmental processes. Arabinose residues could be a component of many polysaccharides, including branched (1→5)-α-arabinans, arabinogalactans in pectic polysaccharides, and arabinoxyloglucans, which are abundant in the cell walls of solanaceous plants. Therefore, to elucidate the role of UAMs and arabinan side chains, we analyzed the UAM RNA interference transformants in tobacco (Nicotiana tabacum L.). The tobacco UAM gene family consists of four members. We generated RNAi transformants (NtUAM-KD) to down-regulate all four of the UAM members. The NtUAM-KD showed abnormal leaf development in the form of a callus-like structure and many holes in the leaf epidermis. A clear reduction in the pectic arabinan content was observed in the tissue of the NtUAM-KD leaf. The arabinose/xylose ratio in the xyloglucan-rich cell wall fraction was drastically reduced in NtUAM-KD. These results suggest that UAMs are required for Ara side chain biosynthesis in both RG-I and AXG in Solanaceae plants, and that arabinan-mediated cell wall networks might be important for normal leaf expansion.

Coimmunoprecipitation of reversibly glycosylated polypeptide with sucrose synthase from developing castor oilseeds

The sucrose synthase (SUS) interactome of developing castor oilseeds (COS; Ricinus communis) was assessed using coimmunoprecipitation (co-IP) with anti-(COS RcSUS1)-IgG followed by proteomic analysis. A 41-kDa polypeptide (p41) that coimmunoprecipitated with RcSUS1 from COS extracts was identified as reversibly glycosylated polypeptide-1 (RcRGP1) by LC-MS/MS and anti-RcRGP1 immunoblotting. Reciprocal Far-western immunodot blotting corroborated the specific interaction between RcSUS1 and RcRGP1. Co-IP using anti-(COS RcSUS1)-IgG and clarified extracts from other developing seeds as well as cluster (proteoid) roots of white lupin and Harsh Hakea consistently recovered 90 kDa SUS polypeptides along with p41/RGP as a SUS interactor. The results suggest that SUS interacts with RGP in diverse sink tissues to channel UDP-glucose derived from imported sucrose into hemicellulose and/or glycoprotein/glycolipid biosynthesis.

Synthesis of a GlcNAcylated arginine building block for the solid phase synthesis of death domain glycopeptide fragments

Herein we describe the synthesis of glycopeptide fragments from the death domains of TRADD and FADD bearing the recently discovered Nω-GlcNAc-β-arginine post-translational modification. TRADD and FADD glycopeptides were accessed through the use of a suitably protected synthetic glycosylamino acid 'cassette' that could be directly incorporated into conventional solid phase peptide synthesis (SPPS) protocols.

X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa

The role of seemingly non-enzymatic proteins in complexes interconverting UDP-arabinopyranose and UDP-arabinofuranose (UDP-arabinosemutases; UAMs) in the plant cytosol remains unknown. To shed light on their function, crystallographic and functional studies of the seemingly non-enzymatic UAM2 protein from Oryza sativa (OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low-dose vector data acquisition. Using size-exclusion chromatography, it is shown that the protein is monomeric in solution. Finally, limited proteolysis was employed to demonstrate DTT-enhanced proteolytic digestion, indicating the existence of at least one intramolecular disulfide bridge or, alternatively, a requirement for a structural metal ion.

Analysis of plant UDP-arabinopyranose mutase (UAM): Role of divalent metals and structure prediction

UDP-arabinopyranose mutase (UAM) is a plant enzyme which interconverts UDP-arabinopyranose (UDP-Arap; a six-membered sugar) to UDP-arabinofuranose (UDP-Araf; a five-membered sugar). Plant mutases belong to a small gene family called Reversibly Glycosylated Proteins (RGPs). So far, UAM has been identified in Oryza sativa (Rice), Arabidopsis thaliana and Hordeum vulgare (Barley). The enzyme requires divalent metal ions for catalytic activity. Here, the divalent metal ion dependency of UAMs from O. sativa (rice) and A. thaliana have been studied using HPLC-based kinetic assays. It was determined that UAM from these species had the highest relative activity in a range of 40-80μM Mn2+. Excess Mn2+ ion concentration decreased the enzyme activity. This trend was observed when other divalent metal ions were used to test activity. To gain a perspective of the role played by the metal ion in activity, an ab initio structural model was generated based on the UAM amino acid sequence and a potential metal binding region was identified. Based on our results, we propose that the probable role of the metal in UAM is stabilizing the diphosphate of the substrate, UDP-Arap.

Genetics, Transcriptional Profiles, and Catalytic Properties of the UDP-Arabinose Mutase Family from Barley

Four members of the UDP-Ara mutase (UAM) gene family from barley have been isolated and characterized, and their map positions on chromosomes 2H, 3H, and 4H have been defined. When the genes are expressed in Escherichia coli, the corresponding HvUAM1, HvUAM2, and HvUAM3 proteins exhibit UAM activity, and the kinetic properties of the enzymes have been determined, including Km, Kcat, and catalytic efficiencies. However, the expressed HvUAM4 protein shows no mutase activity against UDP-Ara or against a broad range of other nucleotide sugars and related molecules. The enzymic data indicate therefore that the HvUAM4 protein may not be a mutase. However, the HvUAM4 gene is transcribed at high levels in all the barley tissues examined, and its transcript abundance is correlated with transcript levels for other genes involved in cell wall biosynthesis. The UDP-l-Arap → UDP-l-Araf reaction, which is essential for the generation of the UDP-Araf substrate for arabinoxylan, arabinogalactan protein, and pectic polysaccharide biosynthesis, is thermodynamically unfavorable and has an equilibrium constant of 0.02. Nevertheless, the incorporation of Araf residues into nascent polysaccharides clearly occurs at biologically appropriate rates. The characterization of the HvUAM genes opens the way for the manipulation of both the amounts and fine structures of heteroxylans in cereals, grasses, and other crop plants, with a view toward enhancing their value in human health and nutrition, and in renewable biofuel production.

Downregulation of a UDP-Arabinomutase Gene in Switchgrass (Panicum virgatum L.) Results in Increased Cell Wall Lignin While Reducing Arabinose-Glycans

Background: Switchgrass (Panicum virgatum L.) is a C₄ perennial prairie grass and a dedicated feedstock for lignocellulosic biofuels. Saccharification and biofuel yields are inhibited by the plant cell wall's natural recalcitrance against enzymatic degradation. Plant hemicellulose polysaccharides such as arabinoxylans structurally support and cross-link other cell wall polymers. Grasses predominately have Type II cell walls that are abundant in arabinoxylan, which comprise nearly 25% of aboveground biomass. A primary component of arabinoxylan synthesis is uridine diphosphate (UDP) linked to arabinofuranose (Araf). A family of UDP-arabinopyranose mutase (UAM)/reversible glycosylated polypeptides catalyze the interconversion between UDP-arabinopyranose (UDP-Arap) and UDP-Araf. Results: The expression of a switchgrass arabinoxylan biosynthesis pathway gene, PvUAM1, was decreased via RNAi to investigate its role in cell wall recalcitrance in the feedstock. PvUAM1 encodes a switchgrass homolog of UDP-arabinose mutase, which converts UDP-Arap to UDP-Araf. Southern blot analysis revealed each transgenic line contained between one to at least seven T-DNA insertions, resulting in some cases, a 95% reduction of native PvUAM1 transcript in stem internodes. Transgenic plants had increased pigmentation in vascular tissues at nodes, but were otherwise similar in morphology to the non-transgenic control. Cell wall-associated arabinose was decreased in leaves and stems by over 50%, but there was an increase in cellulose. In addition, there was a commensurate change in arabinose side chain extension. Cell wall lignin composition was altered with a concurrent increase in lignin content and transcript abundance of lignin biosynthetic genes in mature tillers. Enzymatic saccharification efficiency was unchanged in the transgenic plants relative to the control. Conclusion: Plants with attenuated PvUAM1 transcript had increased cellulose and lignin in cell walls. A decrease in cell wall-associated arabinose was expected, which was likely caused by fewer Araf residues in the arabinoxylan. The decrease in arabinoxylan may cause a compensation response to maintain cell wall integrity by increasing cellulose and lignin biosynthesis. In cases in which increased lignin is desired, e.g., feedstocks for carbon fiber production, downregulated UAM1 coupled with altered expression of other arabinoxylan biosynthesis genes might result in even higher production of lignin in biomass.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010

This review is the sixth update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis.

Oligomerization of the reversibly glycosylated polypeptide: its role during rice plant development and in the regulation of self-glycosylation

A multigenic family of self-glycosylating proteins named reversibly glycosylated polypeptides, designated as RGPs, have been usually associated with carbohydrate metabolism, although they are an enigma both at the functional, as well as at the structural level. In this work, we used biochemical approaches to demonstrate that complex formation is linked to rice plant development, in which class 1 Oryza sativa RGP (OsRGP) would be involved in an early stage of growing plants, while class 2 OsRGP would be associated with a late stage linked to an active polysaccharide synthesis that occurs during the elongation of plant. Here, a further investigation of the complex formation of the Solanum tuberosum RGP (StRGP) was performed. Results showed that disulfide bonds are at least partially responsible for maintaining the oligomeric protein structure, so that the nonreduced StRGP protein showed an apparent higher molecular weight and a lower radioglycosylation of the monomer with respect to its reduced form. Hydrophobic cluster analysis and secondary structure prediction revealed that class 2 RGPs no longer maintained the Rossman fold described for class 1 RGP. A 3D structure of the StRGP protein resolved by homology modeling supports the possibility of intercatenary disulfide bridges formed by exposed cysteines residues C79, C303 and C251 and they are most probably involved in complex formation occurring into the cell cytoplasm.

Rare and unusual glycosylation of peptides and proteins

Glycosylation represents the most complex co- and post-translational modification of proteins. In addition to N- and O-glycans, almost all combinations, including the nature of the carbohydrate moiety and the amino-acid involved, but also the type of the chemical linkage, can be isolated from natural glycoconjugates. This diversity correlates with the importance and the variety of the biological processes (and consequently the diseases) glycosides are involved in. This review focuses on rare and unusual glycosylation of peptides and proteins.

Specific and non-specific enzymes for furanosyl-containing conjugates: biosynthesis, metabolism, and chemo-enzymatic synthesis

There is no doubt now that the synthesis of compounds of varying complexity such as saccharides and derivatives thereof continuously grows with enzymatic methods. This review focuses on recent basic knowledge on enzymes specifically involved in the biosynthesis and degradation of furanosyl-containing polysaccharides and conjugates. Moreover, and when possible, biocatalyzed approaches, alternative to standard synthesis, will be detailed in order to strengthen the high potential of these biocatalysts to go further with the preparation of rare furanosides. Interesting results will be also proposed with chemo-enzymatic processes based on nonfuranosyl-specific enzymes.

Biosynthesis of non-cellulosic polysaccharides of plant cell walls

Enzymes that make the polymer backbones of plant cell wall polysaccharides have proven to be recalcitrant to biochemical purification. Availability of mutational genetics and genomic tools paved the way for rapid progress in identifying genes encoding various cell wall glycan synthases. Mutational genetics, the primary tool used in unraveling cellulose biosynthesis, was ineffective in assigning function to any of the hemicellulosic, polymerizing glycan synthases. A combination of comparative genomics and functional expression in a heterologous system allowed identification of various cellulose synthase-like (Csl) sequences as being involved in the formation of β-1,4-mannan, β-1,4-glucan, and mixed-linked glucan. A number of xylose-deficient mutants have led to a variety of genes, none of which thus far possesses the motifs known to be conserved among polymerizing β-glycan synthases. Except for xylan synthase, which appears to be an agglomerate of proteins just like cellulose synthase, Golgi glycan synthases already identified suggest that the catalytic polypeptide by itself is sufficient for enzyme activity, most likely as a homodimer. Several of the Csl genes remain to be assigned a function. The possibility of the involvement of various Csl genes in making more than one product remains.

Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome

The transcriptome of the developing starchy endosperm of hexaploid wheat (Triticum aestivum) was determined using RNA-Seq isolated at five stages during grain fill. This resource represents an excellent way to identify candidate genes responsible for the starchy endosperm cell wall, which is dominated by arabinoxylan (AX), accounting for 70% of the cell wall polysaccharides, with 20% (1,3;1,4)-β-d-glucan, 7% glucomannan, and 4% cellulose. A complete inventory of transcripts of 124 glycosyltransferase (GT) and 72 glycosylhydrolase (GH) genes associated with cell walls is presented. The most highly expressed GT transcript (excluding those known to be involved in starch synthesis) was a GT47 family transcript similar to Arabidopsis (Arabidopsis thaliana) IRX10 involved in xylan extension, and the second most abundant was a GT61. Profiles for GT43 IRX9 and IRX14 putative orthologs were consistent with roles in AX synthesis. Low abundances were found for transcripts from genes in the acyl-coA transferase BAHD family, for which a role in AX feruloylation has been postulated. The relative expression of these was much greater in whole grain compared with starchy endosperm, correlating with the levels of bound ferulate. Transcripts associated with callose (GSL), cellulose (CESA), pectin (GAUT), and glucomannan (CSLA) synthesis were also abundant in starchy endosperm, while the corresponding cell wall polysaccharides were confirmed as low abundance (glucomannan and callose) or undetectable (pectin) in these samples. Abundant transcripts from GH families associated with the hydrolysis of these polysaccharides were also present, suggesting that they may be rapidly turned over. Abundant transcripts in the GT31 family may be responsible for the addition of Gal residues to arabinogalactan peptide.

Plant nucleotide sugar formation, interconversion, and salvage by sugar recycling

Nucleotide sugars are the universal sugar donors for the formation of polysaccharides, glycoproteins, proteoglycans, glycolipids, and glycosylated secondary metabolites. At least 100 genes encode proteins involved in the formation of nucleotide sugars. These nucleotide sugars are formed using the carbohydrate derived from photosynthesis, the sugar generated by hydrolyzing translocated sucrose, the sugars released from storage carbohydrates, the salvage of sugars from glycoproteins and glycolipids, the recycling of sugars released during primary and secondary cell wall restructuring, and the sugar generated during plant-microbe interactions. Here we emphasize the importance of the salvage of sugars released from glycans for the formation of nucleotide sugars. We also outline how recent studies combining biochemical, genetic, molecular and cellular approaches have led to an increased appreciation of the role nucleotide sugars in all aspects of plant growth and development. Nevertheless, our understanding of these pathways at the single cell level is far from complete.